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Webinar: Dementia and Multimorbidity in Late-Life Disease: Longitudinal and Multimodal Data Science Approaches
- Brenton Pyle
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Hi everyone, I am running Regenie form the RAP Command line. I got tis error "set file : [ukb23158_500k_OQFE.sets.txt.gz] ERROR: unknown chromosome code in set list file". I am using the files already available on UKBiobank RAP.
- Former User of DNAx Community_89
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How to improve the disk speed and data transfer speed in UKB RAP VMs
- Former User of DNAx Community_15
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Is it possible to generate interactive plotly visualizations in the jupyter notebooks on the RAP? I can load the plotly package and can execute the code but I just see a blank where the visualizations should be.
- Former User of DNAx Community_47
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incorporate some additional phenotype variables that are not included here: https://github.com/dnanexus/UKB_RAP/blob/main/end_to_end_gwas_phewas/get-phewas-data.ipynb
- Former User of DNAx Community_42
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Upload permission required in applet
- Former User of DNAx Community_84
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How can I monitor my jobs and get information on how much memory/disk space is being used, which instance was it allocated to, and so on?
- Permanently deleted user
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Rstudio packages: Loading trouble
- Former User of DNAx Community_79
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Are there any annotated gds files available for ukbiobank?
- Former User of DNAx Community_6
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I wrote some JAVA code (jar) which I want to run. How do I do it?
- Former User of DNAx Community_61
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Whats the best way to do simple operations with files while using bash in the RAP?
- Permanently deleted user
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mitochondrial DNA copy number (CN) estimation--how do I do it?
- Former User of DNAx Community_10
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Issue with exporting 'eid' using Table Exporter
- Former User of DNAx Community_5
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PlateID to sample id linker for proteomics data?
- Former User of DNAx Community_6
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Query regarding 200k wgs dataset bgen vs Plink format files?
- Former User of DNAx Community_6
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Low scratch storage space when recoding PLINK files to VCF
- Former User of DNAx Community_5
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Is there a way to skip outputs already generated in WDL?
- Permanently deleted user
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How could we merge exome data (GRch38) and genotype data (GRch37) to explore their LD?
- Former User of DNAx Community_99
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Saige GWAS giving p value/se == 0 for top hits
- Former User of DNAx Community_6
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Is there a way to save locus zoom results generated through locus zoom app into the storage space?
- Former User of DNAx Community_6
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I am trying to run saige and getting this error. Not sure what could be the reason for this. Can you help me out regarding this?
- Former User of DNAx Community_6
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Has anyone faced issues installing the OlinkAnalyze package in R?
- Former User of DNAx Community_6
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Can the proteomics dataset be used as is or do any additional filters need to be applied? How to check qc of the data.
- Former User of DNAx Community_6
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How to access extracted phenotypes?
- Former User of DNAx Community_5
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How to automate phenotype data extraction?
- Former User of DNAx Community_5
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How to filter snpEff.vcf.gz file on UKB RAP?
- Permanently deleted user
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There is a tutorial regarding how to use SAIGE (https://documentation.dnanexus.com/science/scientific-guides/saige-gwas-walkthrough), but here it was not mentioned the GATE (https://github.com/weizhou0/GATE#uk-biobank-gwas-results)
- Former User of DNAx Community_19
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Can I use Haploview on DNAnexus
- Former User of DNAx Community_31
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Hi, I recently noticed that some participants have been automatically removed from the UKB dataset when I updated the dataset. However, I have been working with the previous data, and I want to remove these participants from my datasets
- Former User of DNAx Community_84
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Why there isn't any variant in the VCF file?
- Permanently deleted user
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